Tk:E. coli cut sites: Difference between revisions
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* CTAG sequences in the E. coli genome are rare. | * CTAG sequences in the E. coli genome are rare. | ||
* SpeI cut sites in the E.coli genome: | * SpeI cut sites in the E.coli genome: 79 | ||
* XbaI cut sites in the E. coli genome: 40 | * XbaI cut sites in the E. coli genome: 40 | ||
* Used a 300 Kb region of the E. coli genome as a sample to find the frequency of EcoRI and PstI sites. The 300Kb is random and unimportant. The list is partially complete. All the XbaI and SpeI sites are listed. The # means methylation inhibited -- XbaI by dam: G(mA)TC and SpeI by EcoK: A(mA)CNNNNNNGTGC & GC(mA)CNNNNNNGTT). For the top set, close EcoRI or PstI sites, if any (EcoRI for SpeI cut sites, and PstI for XbaI cut sites). This task is not yet finished. | |||
Line 16: | Line 19: | ||
* 11828 SpeI ACTAGT | * 11828 SpeI ACTAGT EcoRI site at 12890 | ||
* 25681 XbaI TCTAGA | * 25681 XbaI TCTAGA PstI site at 23550 | ||
* 84649 SpeI ACTAGT | * 84649 SpeI ACTAGT No close sites | ||
* 131428 XbaI TCTAGA | * 131428 XbaI TCTAGA PstI 127098 134707; EcoRI 131742 | ||
* 237191 XbaI TCTAGA | * 237191 XbaI TCTAGA PstI 233863; EcoRI 237075 237338 | ||
* 270729 XbaI TCTAGA | * 270729 XbaI TCTAGA PstI 268105 275451; EcoRI 268483 274271 | ||
* 310919 SpeI ACTAGT | * 310919 SpeI ACTAGT PstI 308132 312819; EcoRI 310737 | ||
* 380545 SpeI ACTAGT | * 380545 SpeI ACTAGT No close sites | ||
* 380557 SpeI ACTAGT | * 380557 SpeI ACTAGT PstI 381908; EcoRI 382270 | ||
* 405554 SpeI ACTAGT | * 405554 SpeI ACTAGT PstI 404575; no close EcoRI sites | ||
* 445916 SpeI ACTAGT | * 445916 SpeI ACTAGT PstI 442163; EcoRI 447526 | ||
* 570189 SpeI ACTAGT | * 570189 SpeI ACTAGT PstI 570172; EcoRI 574906 | ||
* 594695 XbaI TCTAGA | * 594695 XbaI TCTAGA PstI 696794; no close EcoRI sites | ||
* 849339 XbaI TCTAGA | * 849339 XbaI TCTAGA PstI 850079; no close EcoRI sites | ||
* 889063 SpeI ACTAGT | * 889063 SpeI ACTAGT No close PstI sites; EcoRI 889113 | ||
* 889173 SpeI ACTAGT | * 889173 SpeI ACTAGT No close PstI sites; EcoRI 889113 | ||
* 921898 XbaI TCTAGA | * 921898 XbaI TCTAGA No close sites | ||
* 968572 SpeI ACTAGT | * 968572 SpeI ACTAGT PstI 972115; EcoRI 966871 | ||
* 1098843 SpeI ACTAGT | * 1098843 SpeI ACTAGT | ||
* 1184031 XbaI TCTAGA | * 1184031 XbaI TCTAGA | ||
Line 59: | Line 62: | ||
* 1755429 XbaI TCTAGA | * 1755429 XbaI TCTAGA | ||
* 1786307 SpeI ACTAGT | * 1786307 SpeI ACTAGT | ||
* 1970292 XbaI TCTAGA | |||
* 2001080 SpeI ACTAGT | |||
* 2009992 XbaI TCTAGA | |||
* 2068219 SpeI ACTAGT | |||
* 2068231 SpeI ACTAGT | |||
* 2088067 SpeI ACTAGT | |||
* 2096253 SpeI ACTAGT | |||
* 2101441 SpeI ACTAGT | |||
* 2104050 XbaI TCTAGA | |||
* 2106663 SpeI ACTAGT | |||
* 2151995 SpeI ACTAGT | |||
* 2152874 XbaI TCTAGA | |||
* 2174649 XbaI TCTAGA | |||
* 2223066 XbaI TCTAGA | |||
* 2310221 SpeI ACTAGT | |||
* 2318050 SpeI ACTAGT | |||
* 2355074 SpeI ACTAGT | |||
* 2493149 SpeI ACTAGT | |||
* 2493548 SpeI ACTAGT | |||
* 2536278 SpeI ACTAGT | |||
* 2558074 XbaI TCTAGA | |||
* 2713371 XbaI TCTAGA | |||
* 2715691 SpeI ACTAGT | |||
* 2727452 XbaI TCTAGA | |||
* 2756439 XbaI TCTAGA | |||
* 2772810 SpeI ACTAGT | |||
* 2781697 SpeI ACTAGT | |||
* 2784977 XbaI TCTAGA | |||
* 2786429 SpeI ACTAGT | |||
* 2808396 SpeI ACTAGT | |||
* 2836247 SpeI ACTAGT | |||
* 2852098 SpeI ACTAGT | |||
* 2901546 SpeI ACTAGT | |||
* 2905982 SpeI ACTAGT | |||
* 2991253 SpeI ACTAGT | |||
* 2991601 XbaI TCTAGA | |||
* 2995637 SpeI ACTAGT | |||
* 2995649 SpeI ACTAGT | |||
* 3031463 SpeI ACTAGT | |||
* 3132842 SpeI ACTAGT | |||
* 3184179 SpeI ACTAGT | |||
* 3184191 SpeI ACTAGT | |||
* 3187097 SpeI ACTAGT | |||
* 3189715 SpeI ACTAGT | |||
* 3382752 SpeI ACTAGT | |||
* 3431660 XbaI TCTAGA | |||
* 3437163 SpeI ACTAGT | |||
* 3457723 SpeI ACTAGT | |||
* 3580870 XbaI TCTAGA | |||
* 3698161 XbaI TCTAGA | |||
* 3741621 SpeI ACTAGT | |||
* 3768516 SpeI ACTAGT | |||
* 3791883 SpeI ACTAGT | |||
* 3804226 XbaI TCTAGA | |||
* 3826538 SpeI ACTAGT | |||
* 3861916 # XbaI TCTAGA | |||
* 3922417 SpeI ACTAGT | |||
* 3929332 SpeI ACTAGT | |||
* 3941469 XbaI TCTAGA | |||
* 4002359 SpeI ACTAGT | |||
* 4166406 XbaI TCTAGA | |||
* 4207808 XbaI TCTAGA | |||
* 4308586 # XbaI TCTAGA | |||
* 4353824 SpeI ACTAGT | |||
* 4395522 SpeI ACTAGT | |||
* 4431187 SpeI ACTAGT | |||
* 4441309 SpeI ACTAGT | |||
* 4496265 SpeI ACTAGT | |||
* 4496277 SpeI ACTAGT | |||
* 4502621 SpeI ACTAGT | |||
* 4505734 XbaI TCTAGA | |||
* 4572269 SpeI ACTAGT | |||
* 4572617 XbaI TCTAGA | |||
* 4578672 XbaI TCTAGA | |||
* 4638702 SpeI ACTAGT |
Latest revision as of 05:40, 4 March 2007
- CTAG sequences in the E. coli genome are rare.
- SpeI cut sites in the E.coli genome: 79
- XbaI cut sites in the E. coli genome: 40
- Used a 300 Kb region of the E. coli genome as a sample to find the frequency of EcoRI and PstI sites. The 300Kb is random and unimportant. The list is partially complete. All the XbaI and SpeI sites are listed. The # means methylation inhibited -- XbaI by dam: G(mA)TC and SpeI by EcoK: A(mA)CNNNNNNGTGC & GC(mA)CNNNNNNGTT). For the top set, close EcoRI or PstI sites, if any (EcoRI for SpeI cut sites, and PstI for XbaI cut sites). This task is not yet finished.
- PstI cut sites in a 300Kbp region of the E. coli genome: 79
- Average length of PstI fragment: 300K/79 = 3800
- We would expect the average length of a double cut XbaI / PstI fragment to be about 1900 bp, and there to be about 40 different ones.
- Likely there are a few with order of 100 bp length
- EcoRI cut sites in a 300Kbp region of the E. coli genome: 42, but 18 are methylation inhibited. 24 are left actually cut.
- Average length of EcoRI fragment: 300K/24 = 12500
- We would expect the average length of the double cut EcoRI / SpeI to be about 6250 bp, and there to be about 79 of them.
- Likely there are a few with order of 80 bp length
- 11828 SpeI ACTAGT EcoRI site at 12890
- 25681 XbaI TCTAGA PstI site at 23550
- 84649 SpeI ACTAGT No close sites
- 131428 XbaI TCTAGA PstI 127098 134707; EcoRI 131742
- 237191 XbaI TCTAGA PstI 233863; EcoRI 237075 237338
- 270729 XbaI TCTAGA PstI 268105 275451; EcoRI 268483 274271
- 310919 SpeI ACTAGT PstI 308132 312819; EcoRI 310737
- 380545 SpeI ACTAGT No close sites
- 380557 SpeI ACTAGT PstI 381908; EcoRI 382270
- 405554 SpeI ACTAGT PstI 404575; no close EcoRI sites
- 445916 SpeI ACTAGT PstI 442163; EcoRI 447526
- 570189 SpeI ACTAGT PstI 570172; EcoRI 574906
- 594695 XbaI TCTAGA PstI 696794; no close EcoRI sites
- 849339 XbaI TCTAGA PstI 850079; no close EcoRI sites
- 889063 SpeI ACTAGT No close PstI sites; EcoRI 889113
- 889173 SpeI ACTAGT No close PstI sites; EcoRI 889113
- 921898 XbaI TCTAGA No close sites
- 968572 SpeI ACTAGT PstI 972115; EcoRI 966871
- 1098843 SpeI ACTAGT
- 1184031 XbaI TCTAGA
- 1195749 SpeI ACTAGT
- 1196554 XbaI TCTAGA
- 1196673 XbaI TCTAGA
- 1198740 XbaI TCTAGA
- 1214824 SpeI ACTAGT
- 1219071 SpeI ACTAGT
- 1321138 SpeI ACTAGT
- 1321146 SpeI ACTAGT
- 1343440 # SpeI ACTAGT
- 1467188 SpeI ACTAGT
- 1467200 SpeI ACTAGT
- 1468285 XbaI TCTAGA
- 1494788 XbaI TCTAGA
- 1522924 SpeI ACTAGT
- 1566793 SpeI ACTAGT
- 1686509 SpeI ACTAGT
- 1695103 SpeI ACTAGT
- 1710491 SpeI ACTAGT
- 1743206 XbaI TCTAGA
- 1745491 SpeI ACTAGT
- 1755429 XbaI TCTAGA
- 1786307 SpeI ACTAGT
- 1970292 XbaI TCTAGA
- 2001080 SpeI ACTAGT
- 2009992 XbaI TCTAGA
- 2068219 SpeI ACTAGT
- 2068231 SpeI ACTAGT
- 2088067 SpeI ACTAGT
- 2096253 SpeI ACTAGT
- 2101441 SpeI ACTAGT
- 2104050 XbaI TCTAGA
- 2106663 SpeI ACTAGT
- 2151995 SpeI ACTAGT
- 2152874 XbaI TCTAGA
- 2174649 XbaI TCTAGA
- 2223066 XbaI TCTAGA
- 2310221 SpeI ACTAGT
- 2318050 SpeI ACTAGT
- 2355074 SpeI ACTAGT
- 2493149 SpeI ACTAGT
- 2493548 SpeI ACTAGT
- 2536278 SpeI ACTAGT
- 2558074 XbaI TCTAGA
- 2713371 XbaI TCTAGA
- 2715691 SpeI ACTAGT
- 2727452 XbaI TCTAGA
- 2756439 XbaI TCTAGA
- 2772810 SpeI ACTAGT
- 2781697 SpeI ACTAGT
- 2784977 XbaI TCTAGA
- 2786429 SpeI ACTAGT
- 2808396 SpeI ACTAGT
- 2836247 SpeI ACTAGT
- 2852098 SpeI ACTAGT
- 2901546 SpeI ACTAGT
- 2905982 SpeI ACTAGT
- 2991253 SpeI ACTAGT
- 2991601 XbaI TCTAGA
- 2995637 SpeI ACTAGT
- 2995649 SpeI ACTAGT
- 3031463 SpeI ACTAGT
- 3132842 SpeI ACTAGT
- 3184179 SpeI ACTAGT
- 3184191 SpeI ACTAGT
- 3187097 SpeI ACTAGT
- 3189715 SpeI ACTAGT
- 3382752 SpeI ACTAGT
- 3431660 XbaI TCTAGA
- 3437163 SpeI ACTAGT
- 3457723 SpeI ACTAGT
- 3580870 XbaI TCTAGA
- 3698161 XbaI TCTAGA
- 3741621 SpeI ACTAGT
- 3768516 SpeI ACTAGT
- 3791883 SpeI ACTAGT
- 3804226 XbaI TCTAGA
- 3826538 SpeI ACTAGT
- 3861916 # XbaI TCTAGA
- 3922417 SpeI ACTAGT
- 3929332 SpeI ACTAGT
- 3941469 XbaI TCTAGA
- 4002359 SpeI ACTAGT
- 4166406 XbaI TCTAGA
- 4207808 XbaI TCTAGA
- 4308586 # XbaI TCTAGA
- 4353824 SpeI ACTAGT
- 4395522 SpeI ACTAGT
- 4431187 SpeI ACTAGT
- 4441309 SpeI ACTAGT
- 4496265 SpeI ACTAGT
- 4496277 SpeI ACTAGT
- 4502621 SpeI ACTAGT
- 4505734 XbaI TCTAGA
- 4572269 SpeI ACTAGT
- 4572617 XbaI TCTAGA
- 4578672 XbaI TCTAGA
- 4638702 SpeI ACTAGT